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In Print: Last Week's Sequencing-Related Papers of Note: Feb 14, 2012


A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq.
Wilbanks EG, Larsen DJ, Neches RY, et al.
Nucleic Acids Res. 2012 Feb 9. [Epub ahead of print]

Summarizing and correcting the GC content bias in high-throughput sequencing.
Benjamin i Y, Speed TP.
Nucleic Acids Res. 2012 Feb 9. [Epub ahead of print]

The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.
Dötsch A, Eckweiler D, Schniederjans M, et al.
PLoS One. 2012;7(2):e31092.

Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types.
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO.
PLoS One. 2012;7(2):e30733.

CAPRG: Sequence assembling pipeline for next generation sequencing of non-model organisms.
Rawat A, Elasri MO, Gust KA, et al.
PLoS One. 2012;7(2):e30370.

Tissue-specific whole transcriptome sequencing in castor, directed at understanding triacylglycerol lipid biosynthetic pathways.
Brown AP, Kroon JT, Swarbreck D, et al.
PLoS One. 2012;7(2):e30100.

Comparison between normalized and unnormalized 454-sequencing libraries for small-scale RNA-seq studies.
Ekblom R, Slate J, Horsburgh GJ, Birkhead T, Burke T.
Comp Funct Genomics. 2012;2012:281693.

The Drosophila melanogaster Genetic Reference Panel.
Mackay TF, Richards S, Stone EA, et al.
Nature. 2012 Feb 8;482(7384):173-8.

Draft genome of the pearl oyster Pinctada fucata: A platform for understanding bivalve biology.
Takeuchi T, Kawashima T, Koyanagi R, et al.
DNA Res. 2012 Feb 6. [Epub ahead of print]

Genome sequence and assembly of Bos indicus.
Canavez FC, Luche DD, Stothard P, et al.
J Hered. 2012 Feb 7. [Epub ahead of print]

Hydrodynamic shearing of DNA in a polymeric microfluidic device.
Nesterova IV, Hupert ML, Witek MA, Soper SA.
Lab Chip. 2012 Feb 7. [Epub ahead of print]

Size evolution and surface characterization of solid-state nanopores in different aqueous solutions.
Li Q, Zhao Q, Lu B, Zhang H, et al.
Nanoscale. 2012 Feb 7. [Epub ahead of print]

Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries.
Dabney J, Meyer M.
Biotechniques. 2012 Feb;52(2):87-94.

Knowledge-based reconstruction of mRNA transcripts with short sequencing reads for transcriptome research.
Seok J, Xu W, Jiang H, Davis RW, Xiao W.
PLoS One. 2012;7(2):e31440.

NGS QC Toolkit: A toolkit for quality control of next generation sequencing data.
Patel RK, Jain M.
PLoS One. 2012;7(2):e30619.

Micrococcal nuclease does not substantially bias nucleosome mapping.
Allan J, Fraser RM, Owen-Hughes T, Keszenman-Pereyra D.
J Mol Biol. 2012 Jan 30. [Epub ahead of print]

De novo analysis and functional classification of the transcriptome of the root lesion nematode, Pratylenchus thornei, after 454 GS FLX sequencing.
Nicol P, Gill R, Fosu-Nyarko J, Jones MG.
Int J Parasitol. 2012 Jan 21. [Epub ahead of print]

The Scan

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.

US Survey Data Suggests Ancestry Testing Leads Way in Awareness, Use of Genetic Testing Awareness

Although roughly three-quarters of surveyed individuals in a Genetics in Medicine study reported awareness of genetic testing, use of such tests was lower and varied with income, ancestry, and disease history.

Coral Genome Leads to Alternative Amino Acid Pathway Found in Other Non-Model Animals

An alternative cysteine biosynthesis pathway unearthed in the Acropora loripes genome subsequently turned up in sequences from non-mammalian, -nematode, or -arthropod animals, researchers report in Science Advances.

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.